The increasing pressure on marine biodiversity emphasizes the importance of finding benchmarks against which to assess change. This is, however, a notoriously difficult task in estuarine ecosystems, where environmental gradients are steep, and where benthic biodiversity is highly variable in space and time. Although recent emphasis on diverse, healthy benthic communities in legislative frameworks has increased the number of indices developed for assessing benthic status, there is a lack of quantitative baselines in benthic diversity that would enable comparisons across broad spatial scales, encompassing different environmental settings and bioregions. By taking advantage of long-term monitoring data, spanning hundreds of stations over the past 40 years, we provide a comprehensive analysis of benthic a, beta, and gamma diversity, encompassing the entire' salinity gradient of the open sea areas of the large, brackish-water Baltic Sea. Using a relatively simple measure, average regional diversity, we define area-specific reference conditions and acceptable deviation against which to gauge current conditions in benthic macrofaunal diversity. Results show a severely impaired condition throughout large areas of the Baltic for the assessment period 2001-2006. All ecosystems are plagued by baselines that shift in time and space, and their definition is not trivial, but average regional diversity may offer a transparent way to deal with such changes in low-diversity systems. Identifying baselines will be of increasing importance given the potential of climatic drivers to interact with local anthropogenic stressors to affect patterns of biodiversity. Our analysis provides an evaluation of the current condition in a system that has been heavily influenced by anthropogenic impact and changing oceanographic conditions, and it provides a basis for future impact assessment and ecosystem-based management.